Volume 20 Issue 9, September 2013

High-throughput RNA sequencing has unveiled the existence of a large number of noncoding antisense RNAs derived from bidirectional promoters; unlike sense transcripts, these RNAs are often unstable. Two recent reports investigate why downstream transcription is productive, whereas upstream transcripts are prone to degradation, revealing that an asymmetric distribution of polyadenylation signals and U1 snRNP–binding sites surrounding transcription start sites control the outcome of bidirectional transcription.

Nucleosome-remodeling factors are instrumental in assembling and disassembling nucleosomes and moving nucleosomes along DNA in a process called nucleosome sliding. This Review summarizes recent progress in understanding of the basic nucleosome sliding mechanism and the interplay of the ATPase and accessory domains in optimizing and regulating nucleosome sliding.

The deubiquitinating enzyme OTUB1 binds charged E2 intermediates and prevents ubiquitin transfer. OTUB1 can also bind uncharged E2, and this interaction is now shown to stimulate OTUB1's deubiquitination activity. Thus, OTUB1–E2 complexes might regulate levels of ubiquitin conjugation in response to available free ubiquitin and the ratio of charged to uncharged E2.

The crystal structure of the full catalytic core of p300 reveals the presence an unexpected RING domain, within the CH2 region, that folds over the HAT-domain substrate-binding pocket. Mutations that destabilize the RING-HAT interaction and increase acetyltransferase activity in vitro are also found in B-cell lymphomas, thus suggesting an important function for this autoinhibitory interaction in vivo.

The activity of PLK1, a key mitotic regulator, is tightly regulated during the cell cycle through both phosphorylation and protein-protein interactions. The crystal structure of PLK1's kinase domain bound to the polo-box domain now provides a structural framework for the regulation of PLK1 through autoinhibition.

Ligand-gated ion channels are susceptible to inactivation upon prolonged exposure to their ligand, a process known as desensitization. A sodium-binding pocket within the KAR-type glutamate receptor GluK2 is now shown to have a crucial role in this process, as desensitization is shown to occur only when the ligand is bound without cation pocket occupancy.

The Arp2/3 complex regulates the actin cytoskeleton by nucleating branched actin filaments in response to cellular signals and is in turn controlled by regulators including GMF. The crystal structure of GMF bound to Arp2/3 provides insight into how GMF inhibits actin nucleation and dissembles branches.

Proteins containing repeats of the WASP homology 2 (WH2) actin-binding module are multifunctional regulators of actin nucleation and assembly. Now biochemical analyses of VopF from Vibrio cholerae reveal a new regulatory mechanism of actin-filament barbed-end dynamics including enhanced nucleation, uncapping and assisted elongation.

Elongation factor G (EF-G) facilitates the movement of tRNA and mRNA by one codon, which is coupled to the ratchet-like rotation of the ribosome complex and is triggered by EF-G–mediated GTP hydrolysis. The crystal structure of pretranslocational ribosome bound to EF-G trapped with a GTP analog provides insight into how the ribosome and EF-G are coordinated to modulate the GTPase activity.

Calmodulin (CaM) regulates a variety of membrane channels in response to Ca2+, but the precise mechanisms are still unclear. Now a combination of single-particle EM, molecular dynamics simulations and functional assays is used to elucidate the structure of Ca2+–CaM bound to the full-length aquaporin AQP0, revealing a cytoplasmic gate that is closed upon CaM binding to control channel permeability in an allosteric manner.

Embryonic stem cells (ESCs) possess a unique chromatin landscape in which 'bivalent' domains of trimethylated histone H3 Lys4 (H3K4me3) and Lys27 (H3K27me3) mark key lineage-specific genes. A new study now reports the identification of Mll2 (KMT2b) as the enzyme responsible for implementing H3K4me3 on bivalently marked promoters in ESCs.

N-terminal acetylases catalyze the cotranslational modification of myriad proteins. Structural and mutational analyses of the NatA complex, comprising a catalytic and auxiliary subunit, and of the catalytic subunit alone reveal the molecular basis for substrate binding, specificity and mode of catalysis, and the role of the auxiliary subunit in these activities.

How plant pri-miRNAs with complex secondary structures are recognized and processed has been unclear. A new study now suggests that unlike canonical processing of pri-miRNAs, terminal loop–branched pri-miRNAs can be processed by Dicer-like 1 (DCL1) complexes bidirectionally, either from the lower stem to the terminal loop or vice versa, resulting in productive and abortive processing of miRNAs, respectively.

Acetylation of the Sir3 N terminus is important for transcriptional silencing in budding yeast and is thought to promote binding of the Sir3 BAH domain to the nucleosome. Structural and biochemical analyses now demonstrate that the acetylated Sir3 N terminus does not interact with the nucleosome directly but instead stabilizes a nucleosome-binding loop in the BAH domain.

N-terminal acetylation of Sir3 is essential for heterochromatin establishment and maintenance in yeast, but its mechanism of action is unknown. The crystal structure of the N-terminally acetylated BAH domain of Sir3 bound to the nucleosome core particle revealed that N-terminal acetylation stabilizes the interaction of Sir3 with the nucleosome.

A mRNA-interactome capture approach in embryonic stem cells (ESCs) has led to the identification of 283 novel RNA-binding protein (RBP) candidates, of which 68 are preferentially expressed in ESCs. Validation of two known E3 ubiquitin ligases as RBPs reveals an intriguing potential link between RNA biology and protein-modification pathways.

Measuring gene expression in individual cells is crucial for understanding the gene regulatory network controlling human embryonic development. Single-cell RNA sequencing (RNA-Seq) analysis of 124 individual cells from human preimplantation embryos and embryonic stem cells (hESCs) now provides a comprehensive framework of the transcriptome landscapes of human early embryos and hESCs.